Examples with IFormatReader loci.formats.IFormatReader used on opensource projects

Example 21 with IFormatReader

use of loci.formats.IFormatReader in project bioformats by openmicroscopy.

the class WrapperTest method createWrappers.

@DataProvider(name = "wrappers")
public Object[][] createWrappers() {
    Location.mapId(TEST_FILE, TEST_FILE);
    Object[][] wrappers = new Object[][] { { new ChannelFiller() }, { new ChannelMerger() }, { new ChannelSeparator() }, { new DimensionSwapper() }, { new FileStitcher() }, { new ImageReader() }, { new MinMaxCalculator() }, { new Memoizer() } };
    for (int i = 0; i < wrappers.length; i++) {
        IFormatReader reader = (IFormatReader) wrappers[i][0];
        try {
            reader.setId(TEST_FILE);
        } catch (FormatException e) {
            e.printStackTrace();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
    return wrappers;
}

Example 22 with IFormatReader

use of loci.formats.IFormatReader in project bioformats by openmicroscopy.

the class PrintLensNA method main.

public static void main(String[] args) throws DependencyException, FormatException, IOException, ServiceException {
    // parse command line arguments
    if (args.length < 1) {
        System.err.println("Usage: java PrintLensNA imageFile");
        System.exit(1);
    }
    String id = args[0];
    // configure reader
    IFormatReader reader = new ImageReader();
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata meta = service.createOMEXMLMetadata();
    reader.setMetadataStore(meta);
    System.out.println("Initializing file: " + id);
    // parse metadata
    reader.setId(id);
    // output metadata values
    int instrumentCount = meta.getInstrumentCount();
    System.out.println("There are " + instrumentCount + " instrument(s) associated with this file");
    for (int i = 0; i < instrumentCount; i++) {
        int objectiveCount = meta.getObjectiveCount(i);
        System.out.println();
        System.out.println("Instrument #" + i + " [" + meta.getInstrumentID(i) + "]: " + objectiveCount + " objective(s) found");
        for (int o = 0; o < objectiveCount; o++) {
            Double lensNA = meta.getObjectiveLensNA(i, o);
            System.out.println("\tObjective #" + o + " [" + meta.getObjectiveID(i, o) + "]: LensNA=" + lensNA);
        }
    }
}

Example 23 with IFormatReader

use of loci.formats.IFormatReader in project bioformats by openmicroscopy.

the class PrintTimestamps method main.

public static void main(String[] args) throws Exception {
    // parse command line arguments
    if (args.length < 1) {
        System.err.println("Usage: java PrintTimestamps imageFile [seriesNo]");
        System.exit(1);
    }
    String id = args[0];
    int series = args.length > 1 ? Integer.parseInt(args[1]) : 0;
    // enable debugging
    // FormatReader.debug = true;
    // create OME-XML metadata store of the latest schema version
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata meta = service.createOMEXMLMetadata();
    // or if you want a specific schema version, you can use:
    // IMetadata meta = service.createOMEXMLMetadata(null, "2009-02");
    // meta.createRoot();
    // create format reader
    IFormatReader reader = new ImageReader();
    reader.setMetadataStore(meta);
    // initialize file
    System.out.println("Initializing " + id);
    reader.setId(id);
    int seriesCount = reader.getSeriesCount();
    if (series < seriesCount)
        reader.setSeries(series);
    series = reader.getSeries();
    System.out.println("\tImage series = " + series + " of " + seriesCount);
    printDimensions(reader);
    printGlobalTiming(meta, series);
    printTimingPerTimepoint(meta, series);
    printTimingPerPlane(meta, series);
}

Example 24 with IFormatReader

use of loci.formats.IFormatReader in project bioformats by openmicroscopy.

the class CropDialog method harvestResults.

@Override
protected boolean harvestResults(GenericDialog gd) {
    final int seriesCount = process.getSeriesCount();
    final IFormatReader r = process.getReader();
    for (int s = 0; s < seriesCount; s++) {
        if (!options.isSeriesOn(s))
            continue;
        r.setSeries(s);
        Region region = new Region();
        region.x = (int) gd.getNextNumber();
        region.y = (int) gd.getNextNumber();
        region.width = (int) gd.getNextNumber();
        region.height = (int) gd.getNextNumber();
        if (region.x < 0)
            region.x = 0;
        if (region.y < 0)
            region.y = 0;
        if (region.x >= r.getSizeX())
            region.x = r.getSizeX() - region.width - 1;
        if (region.y >= r.getSizeY())
            region.y = r.getSizeY() - region.height - 1;
        if (region.width < 1)
            region.width = 1;
        if (region.height < 1)
            region.height = 1;
        if (region.width + region.x > r.getSizeX()) {
            region.width = r.getSizeX() - region.x;
        }
        if (region.height + region.y > r.getSizeY()) {
            region.height = r.getSizeY() - region.y;
        }
        options.setCropRegion(s, region);
    }
    return true;
}

Example 25 with IFormatReader

use of loci.formats.IFormatReader in project bioformats by openmicroscopy.

the class ImagePlusReader method readImage.

private ImagePlus readImage(int s, boolean thumbnail) throws FormatException, IOException {
    final ImporterOptions options = process.getOptions();
    final int zCount = process.getZCount(s);
    final int cCount = process.getCCount(s);
    final int tCount = process.getTCount(s);
    final List<LUT> luts = new ArrayList<LUT>();
    // create image stack
    final ImageStack stack;
    if (options.isVirtual())
        stack = createVirtualStack(process, s, luts);
    else
        stack = readPlanes(process, s, luts, thumbnail);
    notifyListeners(new StatusEvent(1, 1, "Creating image"));
    // create title
    final String seriesName = process.getOMEMetadata().getImageName(s);
    final String file = process.getCurrentFile();
    final IFormatReader reader = process.getReader();
    final String title = constructImageTitle(reader, file, seriesName, options.isGroupFiles());
    // create image
    final ImagePlus imp;
    if (stack.isVirtual()) {
        VirtualImagePlus vip = new VirtualImagePlus(title, stack);
        vip.setReader(reader);
        imp = vip;
        saveLUTs(imp, luts);
    } else
        imp = createImage(title, stack, luts);
    // if concatenating images only store metadata on first series
    if (!options.isConcatenate() || s == 0) {
        final String metadata = process.getOriginalMetadata().toString();
        imp.setProperty("Info", metadata);
    }
    imp.setProperty(PROP_SERIES, s);
    // retrieve the spatial calibration information, if available
    final FileInfo fi = createFileInfo();
    new Calibrator(process).applyCalibration(imp);
    imp.setFileInfo(fi);
    imp.setDimensions(cCount, zCount, tCount);
    // open as a hyperstack, as appropriate
    final boolean hyper = !options.isViewStandard();
    imp.setOpenAsHyperStack(hyper);
    return imp;
}